Method of 3-dimensional imaging of activated samples

Abstract

In one embodiment, an apparatus comprises an optical system with multiple detectors and a processor. The optical system is configured to produce images of an optical source in a first dimension and a second dimension substantially orthogonal to the first dimension at each detector at a given time. Each image from the images is based on an interference of an emission from the optical source in a first direction and an emission from the optical source in a second direction different from the first direction. The processor is configured to calculate a position in a third dimension based on the images. The third dimension is substantially orthogonal to the first dimension and the second dimension.

What is claimed is: 
     
       1. A method comprising:
 activating a first subset of optical labels in a sample; 
 exciting the activated optical labels of the first subset such that optical energy is emitted from the activated optical labels of the first subset in a plurality of directions; 
 interfering the optical energy emitted from the activated optical labels of the first subset in the plurality of directions to produce a plurality of output beams; 
 detecting a plurality of images based on the plurality of output beams, each image from the plurality of images based on an output beam from the plurality of output beams; 
 determining three-dimensional position information of the optical labels of the first subset based on each image from the plurality of images; 
 de-activating the activated optical labels of the first subset so that no further optical signals can be detected for those de-activated optical labels of the first subset; 
 repeating the activating, exciting, interfering, determining, and de-activating for a second subset of optical labels in the sample; 
 wherein each optical label in the first subset and the second subset is separable and identifiable as a sub-diffractive sized point source. 
 
     
     
       2. The method of  claim 1 , wherein de-activating the activated optical labels comprises bleaching the activated optical labels. 
     
     
       3. The method of  claim 2 , wherein bleaching the activated optical labels comprises repeatedly exciting the activated optical labels so that no further optical signals can be detected from those optical labels. 
     
     
       4. The method of  claim 1 , wherein determining three-dimensional position information of the optical labels of the first subset based on each image from the plurality of images comprises forming an image frame sequence from a set of captured image frames. 
     
     
       5. The method of  claim 4 , wherein the image frames are based on optical energy intensities in an x, y plane relating to emission distributions of the activated optical labels. 
     
     
       6. The method of  claim 5 , wherein determining three-dimensional position information of the optical labels of the first subset based on each image from the plurality of images comprises determining three-dimensional position information of the optical labels of the first subset based on an intensity of each image. 
     
     
       7. The method of  claim 5 , further comprising fitting the emission distributions of the activated optical labels to a predetermined distribution to localize the emission distributions of the optical labels in the x, y plane. 
     
     
       8. The method of  claim 7 , further comprising correcting for drift using fiducials included in the image frames. 
     
     
       9. The method of  claim 8 , wherein correcting for drift using fiducials comprises correcting the image frames for drift using the fiducials included in the image frames. 
     
     
       10. The method of  claim 7 , further comprising transforming image frames to produce transformed frames that align with fiducials in the image frames of the image frame sequence in the x, y plane. 
     
     
       11. The method of  claim 10 , further comprising summing image frames captured for each output beam for each position in a z direction into summed image frames. 
     
     
       12. The method of  claim 11 , wherein the summed image frames are a composite of the phase-shifted images frames captured for each output beam. 
     
     
       13. The method of  claim 11 , further comprising fitting the summed image frames to a predetermined distribution to determine centers of the optical labels in the x, y plane. 
     
     
       14. The method of  claim 12 , further comprising:
 fitting the transformed frames to a predetermined distribution; and 
 measuring an amplitude of the emission distribution of the optical label in each frame at the centers of the optical labels in the x, y plane. 
 
     
     
       15. The method of  claim 14 , wherein the center of the optical label is based on a centroid of a distribution representing a likelihood of a location of the optical label. 
     
     
       16. The method of  claim 15 , further comprising normalizing the measured amplitudes to the summed image frames. 
     
     
       17. The method of  claim 16 , obtaining a z plane coordinate of the optical label by correlating the normalized amplitudes with calibration data. 
     
     
       18. The method of  claim 10 , further comprising:
 fitting the transformed frames to a predetermined distribution; and 
 measuring an amplitude of the emission distribution of the optical label in each frame at centers of the optical labels in the x, y plane. 
 
     
     
       19. The method of  claim 1 , wherein activating the first subset of optical labels in the sample comprises activating the first subset of optical labels with an optical source. 
     
     
       20. The method of  claim 19 , wherein the optical source comprises a laser, a light-emitting diode, or an incandescent lamp. 
     
     
       21. The method of  claim 1 , further comprising producing a three-dimensional rendering. 
     
     
       22. The method of  claim 1 , wherein producing the plurality of output beams comprises producing three or more output beams. 
     
     
       23. The method of  claim 22 , wherein the phase difference between an optical energy of a first of the three or more output beams and an optical energy of a second of the three or more output beams is other than 0 degrees or 180 degrees. 
     
     
       24. The method of  claim 1 , wherein the optical labels are labeled molecules within the sample. 
     
     
       25. The method of  claim 24 , wherein the labeled molecules are labeled proteins. 
     
     
       26. The method of  claim 24 , wherein the optical labels include a first labeled protein and a second and different labeled protein. 
     
     
       27. The method of  claim 1 , wherein the optical energy that is emitted from the activated optical labels of the first subset comprises fluorescence.